Multiple sequence alignment - TraesCS6A01G027100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G027100 chr6A 100.000 5285 0 0 1 5285 13671236 13676520 0.000000e+00 9760.0
1 TraesCS6A01G027100 chr6A 76.906 1836 322 60 1169 2929 13733981 13735789 0.000000e+00 948.0
2 TraesCS6A01G027100 chr6A 74.974 979 183 38 1 947 13683095 13684043 1.380000e-105 394.0
3 TraesCS6A01G027100 chr6A 77.280 647 106 33 1215 1840 12926003 12925377 5.070000e-90 342.0
4 TraesCS6A01G027100 chr6A 72.546 601 119 34 1269 1828 12459891 12460486 2.550000e-33 154.0
5 TraesCS6A01G027100 chr6D 92.625 1505 82 22 3558 5047 12318804 12320294 0.000000e+00 2137.0
6 TraesCS6A01G027100 chr6D 88.852 1794 116 29 504 2256 12315337 12317087 0.000000e+00 2128.0
7 TraesCS6A01G027100 chr6D 95.426 1268 48 6 2173 3439 12317088 12318346 0.000000e+00 2012.0
8 TraesCS6A01G027100 chr6D 77.479 1785 301 51 1219 2929 12358143 12359900 0.000000e+00 976.0
9 TraesCS6A01G027100 chr6D 75.305 984 177 35 1 947 12328098 12329052 1.370000e-110 411.0
10 TraesCS6A01G027100 chr6D 78.253 538 77 24 3540 4050 11259597 11260121 5.140000e-80 309.0
11 TraesCS6A01G027100 chr6D 86.585 246 17 1 5040 5285 12320407 12320636 1.890000e-64 257.0
12 TraesCS6A01G027100 chr6D 72.120 599 117 37 1269 1828 11237954 11238541 9.230000e-28 135.0
13 TraesCS6A01G027100 chr6B 94.002 1317 43 15 2177 3471 22585536 22586838 0.000000e+00 1962.0
14 TraesCS6A01G027100 chr6B 91.974 1059 58 13 1219 2251 22584472 22585529 0.000000e+00 1459.0
15 TraesCS6A01G027100 chr6B 89.679 1153 82 16 1 1125 22583318 22584461 0.000000e+00 1435.0
16 TraesCS6A01G027100 chr6B 76.674 1852 313 64 1169 2928 22715512 22717336 0.000000e+00 917.0
17 TraesCS6A01G027100 chr6B 92.339 496 36 1 4554 5047 22588475 22588970 0.000000e+00 704.0
18 TraesCS6A01G027100 chr6B 95.642 413 18 0 3540 3952 22587281 22587693 0.000000e+00 664.0
19 TraesCS6A01G027100 chr6B 95.142 247 11 1 5040 5285 22589083 22589329 6.420000e-104 388.0
20 TraesCS6A01G027100 chr6B 76.040 793 149 18 173 947 22646259 22647028 1.800000e-99 374.0
21 TraesCS6A01G027100 chr6B 92.975 242 12 3 3941 4181 22588059 22588296 1.090000e-91 348.0
22 TraesCS6A01G027100 chr6B 78.545 536 75 25 3540 4048 21133790 21134312 3.070000e-82 316.0
23 TraesCS6A01G027100 chr6B 95.385 130 6 0 4224 4353 22588303 22588432 1.930000e-49 207.0
24 TraesCS6A01G027100 chr6B 71.179 458 107 19 1695 2138 21124847 21125293 2.030000e-14 91.6
25 TraesCS6A01G027100 chr7B 79.528 127 21 4 755 876 115364453 115364579 9.430000e-13 86.1
26 TraesCS6A01G027100 chr4B 81.915 94 12 4 793 882 19036915 19036823 2.040000e-09 75.0
27 TraesCS6A01G027100 chr1A 90.909 44 4 0 833 876 586297071 586297114 5.720000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G027100 chr6A 13671236 13676520 5284 False 9760.000 9760 100.00000 1 5285 1 chr6A.!!$F2 5284
1 TraesCS6A01G027100 chr6A 13733981 13735789 1808 False 948.000 948 76.90600 1169 2929 1 chr6A.!!$F4 1760
2 TraesCS6A01G027100 chr6A 13683095 13684043 948 False 394.000 394 74.97400 1 947 1 chr6A.!!$F3 946
3 TraesCS6A01G027100 chr6A 12925377 12926003 626 True 342.000 342 77.28000 1215 1840 1 chr6A.!!$R1 625
4 TraesCS6A01G027100 chr6D 12315337 12320636 5299 False 1633.500 2137 90.87200 504 5285 4 chr6D.!!$F5 4781
5 TraesCS6A01G027100 chr6D 12358143 12359900 1757 False 976.000 976 77.47900 1219 2929 1 chr6D.!!$F4 1710
6 TraesCS6A01G027100 chr6D 12328098 12329052 954 False 411.000 411 75.30500 1 947 1 chr6D.!!$F3 946
7 TraesCS6A01G027100 chr6D 11259597 11260121 524 False 309.000 309 78.25300 3540 4050 1 chr6D.!!$F2 510
8 TraesCS6A01G027100 chr6B 22715512 22717336 1824 False 917.000 917 76.67400 1169 2928 1 chr6B.!!$F4 1759
9 TraesCS6A01G027100 chr6B 22583318 22589329 6011 False 895.875 1962 93.39225 1 5285 8 chr6B.!!$F5 5284
10 TraesCS6A01G027100 chr6B 22646259 22647028 769 False 374.000 374 76.04000 173 947 1 chr6B.!!$F3 774
11 TraesCS6A01G027100 chr6B 21133790 21134312 522 False 316.000 316 78.54500 3540 4048 1 chr6B.!!$F2 508

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
54 55 0.251474 AAACCTTCCGGGGGCTTAAC 60.251 55.000 13.10 0.00 40.03 2.01 F
57 58 0.468648 CCTTCCGGGGGCTTAACTAG 59.531 60.000 0.00 0.00 0.00 2.57 F
312 329 0.476611 AAAAGGCCTCTCCTCCCACT 60.477 55.000 5.23 0.00 46.94 4.00 F
1213 1276 0.550147 AACCCTAGCCCACATCCACT 60.550 55.000 0.00 0.00 0.00 4.00 F
1214 1277 1.274703 ACCCTAGCCCACATCCACTG 61.275 60.000 0.00 0.00 0.00 3.66 F
2095 2270 1.451651 GCTTGAAAATGTGGAAACGCG 59.548 47.619 3.53 3.53 46.31 6.01 F
2125 2300 2.017049 GTCAGGGTATTCACACATGGC 58.983 52.381 0.00 0.00 0.00 4.40 F
3496 3798 0.039618 TTGCAAGAATCACCCTCCCC 59.960 55.000 0.00 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1162 1225 0.251608 AAACGGAAATGGGGAGTGGG 60.252 55.000 0.00 0.0 0.00 4.61 R
1195 1258 1.082954 AGTGGATGTGGGCTAGGGT 59.917 57.895 0.00 0.0 0.00 4.34 R
1842 1999 1.868997 GTCGCATGGTTCTGTGGTG 59.131 57.895 0.00 0.0 0.00 4.17 R
3176 3471 1.133025 GATTGCCAAATCAGACACGGG 59.867 52.381 0.00 0.0 41.66 5.28 R
3290 3585 1.818674 CACACCTCAATTTAGGGGCAC 59.181 52.381 7.90 0.0 44.63 5.01 R
3477 3779 0.039618 GGGGAGGGTGATTCTTGCAA 59.960 55.000 0.00 0.0 0.00 4.08 R
3999 5070 0.107456 CTGTGGTGGCTCAGTGACTT 59.893 55.000 0.00 0.0 0.00 3.01 R
4748 5838 0.036765 ATGAAAACGAGCGGCCAGTA 60.037 50.000 2.24 0.0 0.00 2.74 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 0.251474 AAACCTTCCGGGGGCTTAAC 60.251 55.000 13.10 0.00 40.03 2.01
57 58 0.468648 CCTTCCGGGGGCTTAACTAG 59.531 60.000 0.00 0.00 0.00 2.57
129 133 6.621737 TCAACGTTAGACTAATAACTTGCG 57.378 37.500 0.00 0.00 34.19 4.85
148 152 3.788694 TGCGACATCAAAACGTCAAAAAG 59.211 39.130 0.00 0.00 32.24 2.27
158 163 5.648178 AAACGTCAAAAAGTAAGGTGGTT 57.352 34.783 0.00 0.00 0.00 3.67
159 164 4.625972 ACGTCAAAAAGTAAGGTGGTTG 57.374 40.909 0.00 0.00 0.00 3.77
160 165 4.263435 ACGTCAAAAAGTAAGGTGGTTGA 58.737 39.130 0.00 0.00 0.00 3.18
161 166 4.701171 ACGTCAAAAAGTAAGGTGGTTGAA 59.299 37.500 0.00 0.00 0.00 2.69
162 167 5.163693 ACGTCAAAAAGTAAGGTGGTTGAAG 60.164 40.000 0.00 0.00 32.86 3.02
163 168 5.163693 CGTCAAAAAGTAAGGTGGTTGAAGT 60.164 40.000 0.00 0.00 0.00 3.01
164 169 6.037391 CGTCAAAAAGTAAGGTGGTTGAAGTA 59.963 38.462 0.00 0.00 0.00 2.24
166 171 8.245491 GTCAAAAAGTAAGGTGGTTGAAGTAAA 58.755 33.333 0.00 0.00 0.00 2.01
168 173 7.949690 AAAAGTAAGGTGGTTGAAGTAAAGT 57.050 32.000 0.00 0.00 0.00 2.66
171 176 6.838382 AGTAAGGTGGTTGAAGTAAAGTGAT 58.162 36.000 0.00 0.00 0.00 3.06
196 213 2.880268 TGAACAAGTCATGCTGGTTGAG 59.120 45.455 12.75 0.00 41.26 3.02
209 226 4.072131 GCTGGTTGAGGTAAAGTGATTCA 58.928 43.478 0.00 0.00 0.00 2.57
265 282 0.673644 ACCTGCAACATGTCGCCTAC 60.674 55.000 6.26 0.00 0.00 3.18
269 286 1.296056 GCAACATGTCGCCTACGGTT 61.296 55.000 0.00 0.00 40.63 4.44
312 329 0.476611 AAAAGGCCTCTCCTCCCACT 60.477 55.000 5.23 0.00 46.94 4.00
314 331 2.039624 GGCCTCTCCTCCCACTGA 59.960 66.667 0.00 0.00 0.00 3.41
321 338 2.836981 CTCTCCTCCCACTGATTTGTCT 59.163 50.000 0.00 0.00 0.00 3.41
330 347 4.248859 CCACTGATTTGTCTTCGATGAGT 58.751 43.478 0.47 0.00 0.00 3.41
332 349 5.869344 CCACTGATTTGTCTTCGATGAGTAA 59.131 40.000 0.47 0.00 0.00 2.24
340 357 4.686091 TGTCTTCGATGAGTAAACAAGCAG 59.314 41.667 0.47 0.00 0.00 4.24
342 359 2.972625 TCGATGAGTAAACAAGCAGGG 58.027 47.619 0.00 0.00 0.00 4.45
365 382 2.818274 GTCGACGGTGGCCATTCC 60.818 66.667 9.72 5.27 0.00 3.01
437 454 9.457436 GGAATAAAGGGAACATACTTGACTAAA 57.543 33.333 0.00 0.00 0.00 1.85
458 475 1.107114 AGACCTCATAGTGCGGTGAG 58.893 55.000 0.00 0.00 41.13 3.51
488 505 4.269363 GGATTAAACACGAGGTATTGGTCG 59.731 45.833 0.00 0.00 42.04 4.79
570 596 1.528076 AGGTGCGTCCATTGTTGCA 60.528 52.632 0.75 0.00 39.02 4.08
575 601 1.885157 CGTCCATTGTTGCATGGCT 59.115 52.632 0.00 0.00 37.84 4.75
679 705 4.650972 TGGCTAAGTATTCAAGGGTGTT 57.349 40.909 0.00 0.00 0.00 3.32
680 706 5.765576 TGGCTAAGTATTCAAGGGTGTTA 57.234 39.130 0.00 0.00 0.00 2.41
796 825 2.125673 CCGGTAAGTGAGTGCGGG 60.126 66.667 0.00 0.00 0.00 6.13
890 919 1.446792 CTGCACGCCGACATCTTCT 60.447 57.895 0.00 0.00 0.00 2.85
892 921 3.084579 CACGCCGACATCTTCTGC 58.915 61.111 0.00 0.00 0.00 4.26
955 990 1.687840 CGTCAGGTCCCCCATGGTA 60.688 63.158 11.73 0.00 34.77 3.25
966 1001 1.212688 CCCCATGGTAGATGCTTGACA 59.787 52.381 11.73 0.00 0.00 3.58
967 1002 2.357050 CCCCATGGTAGATGCTTGACAA 60.357 50.000 11.73 0.00 0.00 3.18
973 1008 2.162408 GGTAGATGCTTGACAACTTGGC 59.838 50.000 0.00 0.00 32.86 4.52
1059 1098 1.069765 GCACGTGATGGGATCCGAT 59.930 57.895 22.23 9.30 0.00 4.18
1090 1129 1.607801 CTGGTGCTGGAGATCGGACA 61.608 60.000 0.00 0.00 0.00 4.02
1104 1144 3.367992 TCGGACAAGCACGTAGTAAAA 57.632 42.857 0.00 0.00 41.61 1.52
1162 1225 0.813210 CCTTCTTCTCCTGCGCATCC 60.813 60.000 12.24 0.00 0.00 3.51
1195 1258 3.294038 TCCGTTTCAACCAAACCCTAA 57.706 42.857 0.00 0.00 41.40 2.69
1199 1262 3.302161 GTTTCAACCAAACCCTAACCCT 58.698 45.455 0.00 0.00 38.86 4.34
1200 1263 4.472496 GTTTCAACCAAACCCTAACCCTA 58.528 43.478 0.00 0.00 38.86 3.53
1201 1264 4.376225 TTCAACCAAACCCTAACCCTAG 57.624 45.455 0.00 0.00 0.00 3.02
1202 1265 2.040679 TCAACCAAACCCTAACCCTAGC 59.959 50.000 0.00 0.00 0.00 3.42
1212 1275 1.141053 CTAACCCTAGCCCACATCCAC 59.859 57.143 0.00 0.00 0.00 4.02
1213 1276 0.550147 AACCCTAGCCCACATCCACT 60.550 55.000 0.00 0.00 0.00 4.00
1214 1277 1.274703 ACCCTAGCCCACATCCACTG 61.275 60.000 0.00 0.00 0.00 3.66
1660 1805 3.737172 GCGTGGCAATTCCGCTGT 61.737 61.111 12.27 0.00 43.21 4.40
1667 1812 1.748493 GGCAATTCCGCTGTATTTGGA 59.252 47.619 0.00 0.00 0.00 3.53
1680 1831 5.123344 GCTGTATTTGGAACGGTATGTCTTT 59.877 40.000 0.00 0.00 0.00 2.52
1842 1999 3.427233 GCATGTGGAGCAATCTTGTCTTC 60.427 47.826 0.00 0.00 0.00 2.87
2095 2270 1.451651 GCTTGAAAATGTGGAAACGCG 59.548 47.619 3.53 3.53 46.31 6.01
2125 2300 2.017049 GTCAGGGTATTCACACATGGC 58.983 52.381 0.00 0.00 0.00 4.40
2340 2599 7.880160 TTTGGAGAATTCATATCATCCGTTT 57.120 32.000 8.44 0.00 0.00 3.60
2349 2608 6.698008 TCATATCATCCGTTTGCAGATTTT 57.302 33.333 0.00 0.00 0.00 1.82
2535 2805 9.349713 TGAACTGTATTTGTCCTGAAAAATAGT 57.650 29.630 3.30 0.00 30.84 2.12
2650 2929 3.712907 GCCCACGCCAGGAACCTA 61.713 66.667 0.00 0.00 0.00 3.08
2673 2952 6.187727 AGATTTGGTTCTCTGTCCTTACAA 57.812 37.500 0.00 0.00 34.49 2.41
2674 2953 6.784031 AGATTTGGTTCTCTGTCCTTACAAT 58.216 36.000 0.00 0.00 34.49 2.71
2690 2969 2.577700 ACAATTGGTTCTTGCACCGTA 58.422 42.857 10.83 0.00 40.09 4.02
2736 3016 6.481644 TGTGGAAATTGGTTGATTTGCTTAAC 59.518 34.615 4.05 0.00 37.95 2.01
2804 3084 7.011482 CCTTACTTTTAAGTATGCGATGCTCTT 59.989 37.037 3.37 0.00 40.87 2.85
3176 3471 5.767816 ACTTGTGTTTTGGACTGGATTAC 57.232 39.130 0.00 0.00 0.00 1.89
3199 3494 2.725759 CGTGTCTGATTTGGCAATCACG 60.726 50.000 0.00 11.41 43.32 4.35
3212 3507 5.417811 TGGCAATCACGCATTATCATTTTT 58.582 33.333 0.00 0.00 0.00 1.94
3285 3580 5.714806 TGATCAACAGTGTAGGTGTCATCTA 59.285 40.000 0.00 0.00 0.00 1.98
3290 3585 6.154203 ACAGTGTAGGTGTCATCTATGATG 57.846 41.667 0.00 1.45 39.30 3.07
3314 3609 3.099141 CCCCTAAATTGAGGTGTGCATT 58.901 45.455 8.14 0.00 34.45 3.56
3324 3619 4.507710 TGAGGTGTGCATTCTATTCTGTC 58.492 43.478 0.00 0.00 0.00 3.51
3401 3703 4.956075 GGACCAAACTTCCCATGTGATATT 59.044 41.667 0.00 0.00 0.00 1.28
3406 3708 7.838696 ACCAAACTTCCCATGTGATATTATTCA 59.161 33.333 0.00 0.00 0.00 2.57
3432 3734 3.904717 TGTTCTACCTTTTGCCCTGAAA 58.095 40.909 0.00 0.00 0.00 2.69
3439 3741 2.548707 CCTTTTGCCCTGAAAGAAAGGC 60.549 50.000 0.00 0.00 45.96 4.35
3471 3773 4.903054 AGTTGCTCACAAGAATCTGATCA 58.097 39.130 0.00 0.00 36.16 2.92
3472 3774 5.498393 AGTTGCTCACAAGAATCTGATCAT 58.502 37.500 0.00 0.00 36.16 2.45
3473 3775 5.944599 AGTTGCTCACAAGAATCTGATCATT 59.055 36.000 0.00 0.00 36.16 2.57
3474 3776 6.093771 AGTTGCTCACAAGAATCTGATCATTC 59.906 38.462 0.00 0.00 36.16 2.67
3475 3777 5.493809 TGCTCACAAGAATCTGATCATTCA 58.506 37.500 10.82 0.00 35.51 2.57
3476 3778 5.941647 TGCTCACAAGAATCTGATCATTCAA 59.058 36.000 10.82 0.00 35.51 2.69
3477 3779 6.602009 TGCTCACAAGAATCTGATCATTCAAT 59.398 34.615 10.82 0.00 35.51 2.57
3478 3780 7.122204 TGCTCACAAGAATCTGATCATTCAATT 59.878 33.333 10.82 3.01 35.51 2.32
3479 3781 7.432545 GCTCACAAGAATCTGATCATTCAATTG 59.567 37.037 10.82 0.00 35.51 2.32
3480 3782 7.255569 TCACAAGAATCTGATCATTCAATTGC 58.744 34.615 10.82 0.00 35.51 3.56
3481 3783 7.033185 CACAAGAATCTGATCATTCAATTGCA 58.967 34.615 10.82 0.00 35.51 4.08
3482 3784 7.544217 CACAAGAATCTGATCATTCAATTGCAA 59.456 33.333 0.00 0.00 35.51 4.08
3483 3785 7.759886 ACAAGAATCTGATCATTCAATTGCAAG 59.240 33.333 4.94 0.00 35.51 4.01
3484 3786 7.640597 AGAATCTGATCATTCAATTGCAAGA 57.359 32.000 4.94 0.00 35.51 3.02
3485 3787 8.063200 AGAATCTGATCATTCAATTGCAAGAA 57.937 30.769 4.94 4.31 35.51 2.52
3486 3788 8.696374 AGAATCTGATCATTCAATTGCAAGAAT 58.304 29.630 4.94 6.69 35.51 2.40
3487 3789 8.873215 AATCTGATCATTCAATTGCAAGAATC 57.127 30.769 4.94 0.00 32.43 2.52
3488 3790 7.399245 TCTGATCATTCAATTGCAAGAATCA 57.601 32.000 4.94 4.48 32.43 2.57
3489 3791 7.255569 TCTGATCATTCAATTGCAAGAATCAC 58.744 34.615 4.94 4.26 32.43 3.06
3490 3792 6.334989 TGATCATTCAATTGCAAGAATCACC 58.665 36.000 4.94 1.91 32.43 4.02
3491 3793 5.075858 TCATTCAATTGCAAGAATCACCC 57.924 39.130 4.94 0.00 32.43 4.61
3492 3794 4.773674 TCATTCAATTGCAAGAATCACCCT 59.226 37.500 4.94 0.00 32.43 4.34
3493 3795 4.789012 TTCAATTGCAAGAATCACCCTC 57.211 40.909 4.94 0.00 0.00 4.30
3494 3796 3.091545 TCAATTGCAAGAATCACCCTCC 58.908 45.455 4.94 0.00 0.00 4.30
3495 3797 2.149973 ATTGCAAGAATCACCCTCCC 57.850 50.000 4.94 0.00 0.00 4.30
3496 3798 0.039618 TTGCAAGAATCACCCTCCCC 59.960 55.000 0.00 0.00 0.00 4.81
3497 3799 1.076705 GCAAGAATCACCCTCCCCC 60.077 63.158 0.00 0.00 0.00 5.40
3535 4197 7.436970 CCCCCAAAAACAATATTATAACGCTTC 59.563 37.037 0.00 0.00 0.00 3.86
3536 4198 7.436970 CCCCAAAAACAATATTATAACGCTTCC 59.563 37.037 0.00 0.00 0.00 3.46
3538 4200 9.019764 CCAAAAACAATATTATAACGCTTCCTG 57.980 33.333 0.00 0.00 0.00 3.86
3597 4275 3.515602 AAAGACAAGGCTGTGAGGATT 57.484 42.857 0.00 0.00 35.30 3.01
3602 4280 4.716784 AGACAAGGCTGTGAGGATTATACA 59.283 41.667 0.00 0.00 35.30 2.29
3652 4330 5.405935 TGAGAGTATTGTTAGCAGCTTCA 57.594 39.130 0.00 0.00 0.00 3.02
3784 4466 7.649533 TGGATCATTTCATACTTCAGCAATT 57.350 32.000 0.00 0.00 0.00 2.32
3857 4541 8.663911 CAGCTATTTTCCTAATAATGCTAGAGC 58.336 37.037 0.00 0.00 42.50 4.09
3860 4544 7.659652 ATTTTCCTAATAATGCTAGAGCGAC 57.340 36.000 0.00 0.00 45.83 5.19
3876 4560 1.670380 GCGACCTGACTTCAGAGGTTC 60.670 57.143 7.87 0.00 46.59 3.62
3964 5035 4.020573 TCGTCACTAATGGAGATTGGTTGT 60.021 41.667 0.00 0.00 31.25 3.32
3999 5070 1.605232 TCGAGCGTGAAGTACTGTTCA 59.395 47.619 0.00 0.00 33.95 3.18
4139 5216 7.551585 TCTGCATTTTTCTTTTGACTTGGTTA 58.448 30.769 0.00 0.00 0.00 2.85
4153 5230 5.125900 TGACTTGGTTAATGCAATGAGATGG 59.874 40.000 0.00 0.00 0.00 3.51
4154 5231 5.018809 ACTTGGTTAATGCAATGAGATGGT 58.981 37.500 0.00 0.00 0.00 3.55
4193 5271 0.593128 CACCCTGTTGTTAGCTGTGC 59.407 55.000 0.00 0.00 0.00 4.57
4201 5279 3.826729 TGTTGTTAGCTGTGCTAGAGAGA 59.173 43.478 0.00 0.00 42.34 3.10
4202 5280 4.082517 TGTTGTTAGCTGTGCTAGAGAGAG 60.083 45.833 0.00 0.00 42.34 3.20
4203 5281 3.956744 TGTTAGCTGTGCTAGAGAGAGA 58.043 45.455 0.00 0.00 42.34 3.10
4204 5282 3.944650 TGTTAGCTGTGCTAGAGAGAGAG 59.055 47.826 0.00 0.00 42.34 3.20
4205 5283 1.392589 AGCTGTGCTAGAGAGAGAGC 58.607 55.000 0.00 0.00 36.99 4.09
4206 5284 0.385390 GCTGTGCTAGAGAGAGAGCC 59.615 60.000 0.00 0.00 37.94 4.70
4207 5285 2.023788 GCTGTGCTAGAGAGAGAGCCT 61.024 57.143 0.00 0.00 37.94 4.58
4208 5286 2.378038 CTGTGCTAGAGAGAGAGCCTT 58.622 52.381 0.00 0.00 37.94 4.35
4209 5287 3.550820 CTGTGCTAGAGAGAGAGCCTTA 58.449 50.000 0.00 0.00 37.94 2.69
4211 5289 4.141287 TGTGCTAGAGAGAGAGCCTTATC 58.859 47.826 0.00 0.00 37.94 1.75
4212 5290 4.141287 GTGCTAGAGAGAGAGCCTTATCA 58.859 47.826 0.00 0.00 37.94 2.15
4213 5291 4.023193 GTGCTAGAGAGAGAGCCTTATCAC 60.023 50.000 0.00 0.00 37.94 3.06
4249 5327 4.355543 TTGCTTGTTCAACTCAGTCAAC 57.644 40.909 0.00 0.00 0.00 3.18
4258 5336 2.246719 ACTCAGTCAACTGTTCTGCC 57.753 50.000 9.82 0.00 44.12 4.85
4320 5398 0.034059 GATGCTGCGCTATACCTGGT 59.966 55.000 9.73 4.05 0.00 4.00
4322 5400 0.179084 TGCTGCGCTATACCTGGTTC 60.179 55.000 9.73 0.00 0.00 3.62
4333 5411 6.706270 CGCTATACCTGGTTCATGTATTCTTT 59.294 38.462 3.84 0.00 30.34 2.52
4398 5476 2.681706 CTGCCGCTTGTAGGAGATATG 58.318 52.381 0.00 0.00 0.00 1.78
4417 5495 9.118300 GAGATATGACCTCATTTCTTGTTGAAT 57.882 33.333 8.96 0.00 42.15 2.57
4478 5556 0.038892 GCTGATGGTGCAAGTTGTGG 60.039 55.000 4.48 0.00 0.00 4.17
4481 5559 1.143889 TGATGGTGCAAGTTGTGGGTA 59.856 47.619 4.48 0.00 0.00 3.69
4489 5567 2.949644 GCAAGTTGTGGGTAGTTTGAGT 59.050 45.455 4.48 0.00 0.00 3.41
4490 5568 3.380320 GCAAGTTGTGGGTAGTTTGAGTT 59.620 43.478 4.48 0.00 0.00 3.01
4514 5592 1.725169 TTTCTGAGGGGTTGGGGGTG 61.725 60.000 0.00 0.00 0.00 4.61
4528 5606 1.151199 GGGGGTGGGGGCATAAATTAT 59.849 52.381 0.00 0.00 0.00 1.28
4566 5656 6.527423 AGTAGTCTTCTTCCTAGATAGGTCG 58.473 44.000 5.82 0.00 44.02 4.79
4574 5664 8.674263 TTCTTCCTAGATAGGTCGTTAACTAG 57.326 38.462 3.71 0.00 44.02 2.57
4607 5697 7.233757 ACAGTTAAGGATGGGATGTATACTCTC 59.766 40.741 4.17 1.28 0.00 3.20
4629 5719 6.656270 TCTCAACATGTTTATGCAATCTCACT 59.344 34.615 8.77 0.00 37.85 3.41
4670 5760 7.968405 ACGAATGTATTACTTTCTTCAAATGGC 59.032 33.333 16.13 0.00 32.14 4.40
4748 5838 4.941263 TCTGGTATTTGCTTGTTTATCGCT 59.059 37.500 0.00 0.00 0.00 4.93
4753 5843 4.678509 TTTGCTTGTTTATCGCTACTGG 57.321 40.909 0.00 0.00 0.00 4.00
4766 5856 0.669318 CTACTGGCCGCTCGTTTTCA 60.669 55.000 0.00 0.00 0.00 2.69
4826 5918 3.622630 TCTACTAGCTGGGTCTCTGTTC 58.377 50.000 0.85 0.00 0.00 3.18
4838 5930 0.388649 CTCTGTTCTCGTTGGTCCCG 60.389 60.000 0.00 0.00 0.00 5.14
4860 5952 1.538687 GGCAGCAGCTGGGTTTCATT 61.539 55.000 24.13 0.00 41.70 2.57
4862 5954 0.389426 CAGCAGCTGGGTTTCATTGC 60.389 55.000 17.12 0.00 36.62 3.56
4873 5965 2.034076 GTTTCATTGCGTCGTGTGTTC 58.966 47.619 0.00 0.00 0.00 3.18
4881 5973 1.227853 GTCGTGTGTTCTGGGGCTT 60.228 57.895 0.00 0.00 0.00 4.35
4887 5979 1.064017 TGTGTTCTGGGGCTTGACTTT 60.064 47.619 0.00 0.00 0.00 2.66
4941 6033 1.243902 GCTTTTCGTCCATTGTCCCA 58.756 50.000 0.00 0.00 0.00 4.37
4982 6074 0.250124 TGTTGTGGTTGGTAGGAGCG 60.250 55.000 0.00 0.00 0.00 5.03
4990 6082 2.104530 GGTAGGAGCGTCGCTTCC 59.895 66.667 22.67 21.73 39.88 3.46
5055 6267 6.580167 TCTTATCCAATAGGTCATATCCCCA 58.420 40.000 0.00 0.00 35.89 4.96
5059 6271 3.652869 CCAATAGGTCATATCCCCAGTGT 59.347 47.826 0.00 0.00 0.00 3.55
5066 6278 2.771943 TCATATCCCCAGTGTCCAAGTC 59.228 50.000 0.00 0.00 0.00 3.01
5067 6279 2.335681 TATCCCCAGTGTCCAAGTCA 57.664 50.000 0.00 0.00 0.00 3.41
5072 6284 0.939577 CCAGTGTCCAAGTCACGTCG 60.940 60.000 0.00 0.00 40.28 5.12
5075 6287 0.529119 GTGTCCAAGTCACGTCGGTT 60.529 55.000 0.00 0.00 0.00 4.44
5104 6316 8.118976 AGGTTACCTTATTTACCTTTGCTTTC 57.881 34.615 0.00 0.00 37.75 2.62
5107 6319 5.399113 ACCTTATTTACCTTTGCTTTCCCA 58.601 37.500 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 4.083537 TGGCAAAGCACAAATACGAACTAG 60.084 41.667 0.00 0.00 0.00 2.57
57 58 3.006659 TGGCAAAGCACAAATACGAAC 57.993 42.857 0.00 0.00 0.00 3.95
129 133 6.970613 ACCTTACTTTTTGACGTTTTGATGTC 59.029 34.615 0.00 0.00 35.67 3.06
148 152 7.227910 TGAATCACTTTACTTCAACCACCTTAC 59.772 37.037 0.00 0.00 0.00 2.34
158 163 8.450578 ACTTGTTCATGAATCACTTTACTTCA 57.549 30.769 12.12 0.00 33.75 3.02
159 164 8.559536 TGACTTGTTCATGAATCACTTTACTTC 58.440 33.333 12.12 0.00 0.00 3.01
160 165 8.450578 TGACTTGTTCATGAATCACTTTACTT 57.549 30.769 12.12 0.00 0.00 2.24
161 166 8.627208 ATGACTTGTTCATGAATCACTTTACT 57.373 30.769 12.12 0.00 43.87 2.24
196 213 5.506317 GCATACTGGCATGAATCACTTTACC 60.506 44.000 0.00 0.00 0.00 2.85
243 260 0.878416 GGCGACATGTTGCAGGTTTA 59.122 50.000 33.55 0.00 41.74 2.01
244 261 0.823356 AGGCGACATGTTGCAGGTTT 60.823 50.000 33.55 14.36 41.74 3.27
312 329 7.571244 GCTTGTTTACTCATCGAAGACAAATCA 60.571 37.037 0.00 0.00 42.51 2.57
314 331 6.204688 TGCTTGTTTACTCATCGAAGACAAAT 59.795 34.615 0.00 0.00 42.51 2.32
321 338 3.334691 CCCTGCTTGTTTACTCATCGAA 58.665 45.455 0.00 0.00 0.00 3.71
330 347 1.960689 GACCTTTGCCCTGCTTGTTTA 59.039 47.619 0.00 0.00 0.00 2.01
332 349 1.455383 CGACCTTTGCCCTGCTTGTT 61.455 55.000 0.00 0.00 0.00 2.83
340 357 3.047877 CACCGTCGACCTTTGCCC 61.048 66.667 10.58 0.00 0.00 5.36
342 359 3.723348 GCCACCGTCGACCTTTGC 61.723 66.667 10.58 4.50 0.00 3.68
365 382 3.515502 TGGACCTTCACATACAAGAGAGG 59.484 47.826 0.00 0.00 0.00 3.69
458 475 5.019785 ACCTCGTGTTTAATCCTATGGTC 57.980 43.478 0.00 0.00 0.00 4.02
570 596 4.764143 GGTGCTTAACCCAGCCAT 57.236 55.556 0.00 0.00 44.02 4.40
659 685 4.569564 CGTAACACCCTTGAATACTTAGCC 59.430 45.833 0.00 0.00 0.00 3.93
679 705 3.558931 TCGACTACTTGGATACCCGTA 57.441 47.619 0.00 0.00 34.29 4.02
680 706 2.425143 TCGACTACTTGGATACCCGT 57.575 50.000 0.00 0.00 34.29 5.28
730 759 2.657237 CCGAGGCACTTCTCCGTT 59.343 61.111 0.00 0.00 41.55 4.44
733 762 2.896443 CTCCCGAGGCACTTCTCC 59.104 66.667 0.00 0.00 41.55 3.71
796 825 2.802106 CTCCTCGCGGACCTCTTC 59.198 66.667 6.13 0.00 34.92 2.87
884 913 4.845580 CCGCCGCCTGCAGAAGAT 62.846 66.667 17.39 0.00 41.33 2.40
947 976 2.684881 GTTGTCAAGCATCTACCATGGG 59.315 50.000 18.09 0.00 0.00 4.00
955 990 0.877071 CGCCAAGTTGTCAAGCATCT 59.123 50.000 1.45 0.00 0.00 2.90
1019 1055 4.504858 CCAACATGTCTCCCTGTACTTAC 58.495 47.826 0.00 0.00 0.00 2.34
1059 1098 2.429930 CACCAGCCCAGTTCGGAA 59.570 61.111 0.00 0.00 36.56 4.30
1090 1129 2.089201 GGCCCATTTTACTACGTGCTT 58.911 47.619 0.00 0.00 0.00 3.91
1129 1169 4.402829 AGAAGAAGGAAGGAAGGAAAAGC 58.597 43.478 0.00 0.00 0.00 3.51
1130 1170 5.007034 GGAGAAGAAGGAAGGAAGGAAAAG 58.993 45.833 0.00 0.00 0.00 2.27
1162 1225 0.251608 AAACGGAAATGGGGAGTGGG 60.252 55.000 0.00 0.00 0.00 4.61
1195 1258 1.082954 AGTGGATGTGGGCTAGGGT 59.917 57.895 0.00 0.00 0.00 4.34
1212 1275 3.518998 ATCTCGTCGCCGTCCCAG 61.519 66.667 0.00 0.00 35.01 4.45
1213 1276 3.822192 CATCTCGTCGCCGTCCCA 61.822 66.667 0.00 0.00 35.01 4.37
1214 1277 4.570663 CCATCTCGTCGCCGTCCC 62.571 72.222 0.00 0.00 35.01 4.46
1272 1357 3.267908 GAGGTTCTCGTCCTCCAGA 57.732 57.895 0.98 0.00 43.90 3.86
1354 1442 4.503314 GCGCTCCCATTGCTTGGC 62.503 66.667 0.00 0.00 44.97 4.52
1660 1805 5.413213 CACCAAAGACATACCGTTCCAAATA 59.587 40.000 0.00 0.00 0.00 1.40
1667 1812 2.874457 GCTCCACCAAAGACATACCGTT 60.874 50.000 0.00 0.00 0.00 4.44
1680 1831 3.150949 CAGACCACAGCTCCACCA 58.849 61.111 0.00 0.00 0.00 4.17
1842 1999 1.868997 GTCGCATGGTTCTGTGGTG 59.131 57.895 0.00 0.00 0.00 4.17
1994 2169 5.482006 TGTTGATAGAGTTGATGTCCACAG 58.518 41.667 0.00 0.00 0.00 3.66
1997 2172 4.507710 GCTGTTGATAGAGTTGATGTCCA 58.492 43.478 0.00 0.00 0.00 4.02
2095 2270 4.098196 GTGAATACCCTGACTACTGACCTC 59.902 50.000 0.00 0.00 0.00 3.85
2125 2300 2.812591 AGACAACAATCTTCTGCAGCAG 59.187 45.455 17.10 17.10 0.00 4.24
2349 2608 7.759489 AGATAAACAATTACCTGCAGTGAAA 57.241 32.000 13.81 4.01 0.00 2.69
2535 2805 7.353414 TCAAACAAATGGTCAAAATAGTCCA 57.647 32.000 0.00 0.00 0.00 4.02
2650 2929 5.825593 TGTAAGGACAGAGAACCAAATCT 57.174 39.130 0.00 0.00 0.00 2.40
2673 2952 2.264005 TGTACGGTGCAAGAACCAAT 57.736 45.000 0.00 0.00 40.53 3.16
2674 2953 2.039818 TTGTACGGTGCAAGAACCAA 57.960 45.000 7.59 0.00 40.53 3.67
2724 3004 8.840833 TGACTACACTTATGTTAAGCAAATCA 57.159 30.769 0.00 0.00 40.48 2.57
2736 3016 4.579869 AGGTGCCTTTGACTACACTTATG 58.420 43.478 0.00 0.00 33.53 1.90
2772 3052 6.373216 TCGCATACTTAAAAGTAAGGTGCAAT 59.627 34.615 19.30 0.00 44.72 3.56
2773 3053 5.701750 TCGCATACTTAAAAGTAAGGTGCAA 59.298 36.000 19.30 5.91 44.72 4.08
2775 3055 5.789710 TCGCATACTTAAAAGTAAGGTGC 57.210 39.130 13.34 13.34 44.03 5.01
2777 3057 6.113411 AGCATCGCATACTTAAAAGTAAGGT 58.887 36.000 6.66 0.00 44.03 3.50
2778 3058 6.480320 AGAGCATCGCATACTTAAAAGTAAGG 59.520 38.462 6.66 4.17 42.05 2.69
2780 3060 7.843490 AAGAGCATCGCATACTTAAAAGTAA 57.157 32.000 6.66 0.00 42.05 2.24
2781 3061 8.936070 TTAAGAGCATCGCATACTTAAAAGTA 57.064 30.769 5.11 5.11 42.59 2.24
2794 3074 1.894282 GCCCCCTTAAGAGCATCGC 60.894 63.158 3.36 0.00 42.67 4.58
2892 3175 2.692041 GAGCTGGGCAAAAGAATGCTAT 59.308 45.455 0.00 0.00 45.68 2.97
2903 3189 1.486310 ACAATATCGAGAGCTGGGCAA 59.514 47.619 0.00 0.00 0.00 4.52
3070 3365 8.065473 ACAATTGATTATCAGCCACACAAATA 57.935 30.769 13.59 0.00 0.00 1.40
3072 3367 6.343716 ACAATTGATTATCAGCCACACAAA 57.656 33.333 13.59 0.00 0.00 2.83
3176 3471 1.133025 GATTGCCAAATCAGACACGGG 59.867 52.381 0.00 0.00 41.66 5.28
3285 3580 3.052642 ACCTCAATTTAGGGGCACATCAT 60.053 43.478 10.43 0.00 41.32 2.45
3290 3585 1.818674 CACACCTCAATTTAGGGGCAC 59.181 52.381 7.90 0.00 44.63 5.01
3401 3703 5.334569 GCAAAAGGTAGAACAAGCGTGAATA 60.335 40.000 6.65 0.00 0.00 1.75
3406 3708 1.607148 GGCAAAAGGTAGAACAAGCGT 59.393 47.619 0.00 0.00 0.00 5.07
3432 3734 0.695347 ACTTGCTAGCCTGCCTTTCT 59.305 50.000 13.29 0.00 0.00 2.52
3458 3760 7.973944 TCTTGCAATTGAATGATCAGATTCTTG 59.026 33.333 10.34 4.46 36.78 3.02
3465 3767 6.475727 GGTGATTCTTGCAATTGAATGATCAG 59.524 38.462 16.22 0.00 36.78 2.90
3471 3773 4.161001 GGAGGGTGATTCTTGCAATTGAAT 59.839 41.667 10.34 12.35 35.83 2.57
3472 3774 3.511146 GGAGGGTGATTCTTGCAATTGAA 59.489 43.478 10.34 0.92 0.00 2.69
3473 3775 3.091545 GGAGGGTGATTCTTGCAATTGA 58.908 45.455 10.34 0.00 0.00 2.57
3474 3776 2.167075 GGGAGGGTGATTCTTGCAATTG 59.833 50.000 0.00 0.00 0.00 2.32
3475 3777 2.460669 GGGAGGGTGATTCTTGCAATT 58.539 47.619 0.00 0.00 0.00 2.32
3476 3778 1.342374 GGGGAGGGTGATTCTTGCAAT 60.342 52.381 0.00 0.00 0.00 3.56
3477 3779 0.039618 GGGGAGGGTGATTCTTGCAA 59.960 55.000 0.00 0.00 0.00 4.08
3478 3780 1.691219 GGGGAGGGTGATTCTTGCA 59.309 57.895 0.00 0.00 0.00 4.08
3479 3781 1.076705 GGGGGAGGGTGATTCTTGC 60.077 63.158 0.00 0.00 0.00 4.01
3509 3811 6.811954 AGCGTTATAATATTGTTTTTGGGGG 58.188 36.000 0.00 0.00 0.00 5.40
3510 3812 7.436970 GGAAGCGTTATAATATTGTTTTTGGGG 59.563 37.037 0.00 0.00 0.00 4.96
3511 3813 8.194769 AGGAAGCGTTATAATATTGTTTTTGGG 58.805 33.333 0.00 0.00 0.00 4.12
3512 3814 9.019764 CAGGAAGCGTTATAATATTGTTTTTGG 57.980 33.333 0.00 0.00 0.00 3.28
3513 3815 9.019764 CCAGGAAGCGTTATAATATTGTTTTTG 57.980 33.333 0.00 0.00 0.00 2.44
3517 4179 8.691661 ATTCCAGGAAGCGTTATAATATTGTT 57.308 30.769 8.20 0.00 0.00 2.83
3519 4181 9.965824 AAAATTCCAGGAAGCGTTATAATATTG 57.034 29.630 8.20 0.00 0.00 1.90
3532 4194 4.281688 ACATCCACACAAAATTCCAGGAAG 59.718 41.667 8.20 0.00 0.00 3.46
3535 4197 3.573538 TGACATCCACACAAAATTCCAGG 59.426 43.478 0.00 0.00 0.00 4.45
3536 4198 4.852134 TGACATCCACACAAAATTCCAG 57.148 40.909 0.00 0.00 0.00 3.86
3538 4200 4.039124 ACCTTGACATCCACACAAAATTCC 59.961 41.667 0.00 0.00 0.00 3.01
3753 4435 9.166173 CTGAAGTATGAAATGATCCAAACAGTA 57.834 33.333 0.00 0.00 0.00 2.74
3755 4437 6.971184 GCTGAAGTATGAAATGATCCAAACAG 59.029 38.462 0.00 0.00 0.00 3.16
3821 4505 8.635765 ATTAGGAAAATAGCTGAACAAACTCA 57.364 30.769 0.00 0.00 0.00 3.41
3857 4541 1.613925 TGAACCTCTGAAGTCAGGTCG 59.386 52.381 8.42 0.00 42.61 4.79
3860 4544 2.630098 TGACTGAACCTCTGAAGTCAGG 59.370 50.000 8.42 0.00 43.01 3.86
3876 4560 8.950210 ACTTCACCACTATGAAATTAATGACTG 58.050 33.333 0.00 0.00 38.12 3.51
3964 5035 1.872237 GCTCGAACAGTACCTGTGCAA 60.872 52.381 3.41 0.00 44.62 4.08
3999 5070 0.107456 CTGTGGTGGCTCAGTGACTT 59.893 55.000 0.00 0.00 0.00 3.01
4080 5157 5.336150 TGCAGAATTGGAAAGTTCAACAA 57.664 34.783 0.00 0.00 0.00 2.83
4123 5200 7.495901 TCATTGCATTAACCAAGTCAAAAGAA 58.504 30.769 0.00 0.00 0.00 2.52
4128 5205 6.350361 CCATCTCATTGCATTAACCAAGTCAA 60.350 38.462 0.00 0.00 0.00 3.18
4130 5207 5.126061 ACCATCTCATTGCATTAACCAAGTC 59.874 40.000 0.00 0.00 0.00 3.01
4139 5216 4.338012 TGAGTCAACCATCTCATTGCATT 58.662 39.130 0.00 0.00 36.04 3.56
4181 5258 4.336280 TCTCTCTCTAGCACAGCTAACAA 58.664 43.478 0.01 0.00 40.82 2.83
4182 5259 3.944650 CTCTCTCTCTAGCACAGCTAACA 59.055 47.826 0.01 0.00 40.82 2.41
4193 5271 6.321181 ACAAAGTGATAAGGCTCTCTCTCTAG 59.679 42.308 0.00 0.00 0.00 2.43
4201 5279 5.753721 AAGAGACAAAGTGATAAGGCTCT 57.246 39.130 0.00 0.00 33.27 4.09
4202 5280 8.499403 AATAAAGAGACAAAGTGATAAGGCTC 57.501 34.615 0.00 0.00 0.00 4.70
4203 5281 8.870075 AAATAAAGAGACAAAGTGATAAGGCT 57.130 30.769 0.00 0.00 0.00 4.58
4204 5282 9.346725 CAAAATAAAGAGACAAAGTGATAAGGC 57.653 33.333 0.00 0.00 0.00 4.35
4205 5283 9.346725 GCAAAATAAAGAGACAAAGTGATAAGG 57.653 33.333 0.00 0.00 0.00 2.69
4208 5286 9.897744 CAAGCAAAATAAAGAGACAAAGTGATA 57.102 29.630 0.00 0.00 0.00 2.15
4209 5287 8.416329 ACAAGCAAAATAAAGAGACAAAGTGAT 58.584 29.630 0.00 0.00 0.00 3.06
4211 5289 7.992180 ACAAGCAAAATAAAGAGACAAAGTG 57.008 32.000 0.00 0.00 0.00 3.16
4212 5290 8.250332 TGAACAAGCAAAATAAAGAGACAAAGT 58.750 29.630 0.00 0.00 0.00 2.66
4213 5291 8.633075 TGAACAAGCAAAATAAAGAGACAAAG 57.367 30.769 0.00 0.00 0.00 2.77
4320 5398 8.690884 TCCACACAAAAAGAAAGAATACATGAA 58.309 29.630 0.00 0.00 0.00 2.57
4322 5400 8.870160 TTCCACACAAAAAGAAAGAATACATG 57.130 30.769 0.00 0.00 0.00 3.21
4333 5411 8.006298 AGACATATTGTTTCCACACAAAAAGA 57.994 30.769 0.00 0.00 40.07 2.52
4398 5476 7.206981 TCAGAATTCAACAAGAAATGAGGTC 57.793 36.000 8.44 0.00 40.22 3.85
4440 5518 1.633945 GCCCTAGGGAAAAAGTGGAGA 59.366 52.381 33.21 0.00 37.50 3.71
4507 5585 1.531981 AATTTATGCCCCCACCCCCA 61.532 55.000 0.00 0.00 0.00 4.96
4514 5592 3.089284 CCCTCGAATAATTTATGCCCCC 58.911 50.000 0.00 0.00 0.00 5.40
4566 5656 7.661040 TCCTTAACTGTACCACACTAGTTAAC 58.339 38.462 8.93 0.00 36.68 2.01
4574 5664 3.262405 TCCCATCCTTAACTGTACCACAC 59.738 47.826 0.00 0.00 0.00 3.82
4607 5697 7.529158 TGTAGTGAGATTGCATAAACATGTTG 58.471 34.615 12.82 1.19 0.00 3.33
4659 5749 3.420893 CAAGTGTAGGGCCATTTGAAGA 58.579 45.455 6.18 0.00 34.91 2.87
4748 5838 0.036765 ATGAAAACGAGCGGCCAGTA 60.037 50.000 2.24 0.00 0.00 2.74
4753 5843 0.247301 CTTCGATGAAAACGAGCGGC 60.247 55.000 0.00 0.00 43.55 6.53
4766 5856 2.026822 ACCAAAGTCCATGAGCTTCGAT 60.027 45.455 0.00 0.00 0.00 3.59
4850 5942 0.816018 ACACGACGCAATGAAACCCA 60.816 50.000 0.00 0.00 0.00 4.51
4860 5952 2.279851 CCCAGAACACACGACGCA 60.280 61.111 0.00 0.00 0.00 5.24
4862 5954 2.989055 AAGCCCCAGAACACACGACG 62.989 60.000 0.00 0.00 0.00 5.12
4873 5965 1.341209 GGAAACAAAGTCAAGCCCCAG 59.659 52.381 0.00 0.00 0.00 4.45
4963 6055 0.250124 CGCTCCTACCAACCACAACA 60.250 55.000 0.00 0.00 0.00 3.33
4967 6059 1.445582 CGACGCTCCTACCAACCAC 60.446 63.158 0.00 0.00 0.00 4.16
4968 6060 2.967397 CGACGCTCCTACCAACCA 59.033 61.111 0.00 0.00 0.00 3.67
5055 6267 1.362717 CCGACGTGACTTGGACACT 59.637 57.895 0.00 0.00 36.29 3.55
5059 6271 2.027003 AAAAACCGACGTGACTTGGA 57.973 45.000 0.00 0.00 0.00 3.53
5066 6278 3.392882 AGGTAACCTAAAAACCGACGTG 58.607 45.455 0.00 0.00 38.37 4.49
5067 6279 3.751479 AGGTAACCTAAAAACCGACGT 57.249 42.857 0.00 0.00 38.37 4.34
5075 6287 9.590828 AGCAAAGGTAAATAAGGTAACCTAAAA 57.409 29.630 0.00 0.00 41.51 1.52
5104 6316 0.478507 AAAGGAGAGGGTTGTGTGGG 59.521 55.000 0.00 0.00 0.00 4.61


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.